Here are some 194 of the phylogeny packages, and 16 free servers, that I know about. It is an attempt to be completely comprehensive. I have not made any attempt to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made about twice a year (however, almost no updates have been made since the start of 2001, and this will continue until at least the end of 2002 when I hope to complete a major writing project). Some of these programs are available over Internet from ftp server machines, or by World Wide Web.
The programs listed below include both free and non-free ones; in some cases I do not know whether a program is free. I have listed as free those that I knew were free; for the others you have to ask their distributor.
If you discover any inaccuracies, or feel that I have left any important
programs or facts out, or if links do not work properly, please
e-mail me at: (
|List of packages arranged ...|
|Table of contents by methods available|
Distance matrix methods
Computation of distances
Maximum likelihood and related methods
Invariants (or Evolutionary Parsimony) methods
Interactive tree manipulation
Looking for hybridization or recombination events
Bootstrapping and other measures of support
Consensus trees and distances between trees
Tree-based sequence alignment
Biogeographic analysis and host-parasite comparison
Comparative method analysis
Simulation of trees or data
Examination of shapes of trees
Clocks, dating and stratigraphy
Description or prediction of data from trees
Sequence management/job submission
Teaching about phylogenies
Table of contents by computer systems
on which they work
|Analyzing particular types of data|
Here you will find lists of programs that analyze types of data other than molecular sequence data. We will gradually expand this list of data types.
Here are the packages that have most recently been added to these listings: (the most recent ones first). Entries are retained in this list for about 6 months.
Here are the packages whose entries have most recently been changed: The date on which each change was entered is shown. Entries are retained in this list for about 6 months. (Note that changes may be as small as updated version numbers or a modified web address). The most recent changes are first.
|Other lists of phylogeny software|
http://www.ucmp.berkeley.edu/subway/phylo/phylosoft.html. Few programs are listed, but there is a very nice list of software lists there.
http://www.pasteur.fr/recherche/BNB/bnb-en.html. Programs for phylogenies can be found by, for example, selecting software from the Resource Type list and evolution from the Biological Domain list without selecting any Organism.
http://www.pitt.edu/~csna/software.html. Note, however, that inferring phylogenies and making clusters are different tasks; the software described on that list will be of most use to people who are trying to cluster or classify but not to infer phylogenies.
http://genamics.com/software/index.htmin a number of categories. One of them is Phylogenetic Analysis. They have a reasonably large number of entries under that heading, though it also includes some statistical genetics software that is really not phylogenetic. Their listing has links to the web sites of the software; for those programs that are not available by Web they maintain copies for download at their server.
http://grinch.zoo.ox.ac.uk/RAP_links.htmllisting programs and their web sites that test for the presence of recombination or hybridization events in DNA sequence data. It lists some programs that are covered here, and others that are outside the scope of these web pages.
bioinformatik.deindex of resources. It includes a list of software located at
http://www.bioinformatik.de/cgi-bin/browse/Catalog/Software. The phylogeny programs listings there are located within the categories for different operating systems.
http://phylogeny.arizona.edu/tree/programs/programs.html. This list has not been updated in a while.
http://www.bis.med.jhmi.edu/Dan/software/biol-links.html. It has not, as far as I know, been updated in a while.
To first page of main software listing